Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009013.1 Kokia drynarioides strain JFW-HI SEQ_123711, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 18223
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:202 original size:60 final size:60

Alignment explanation


    Indices: 119--454  Score: 313
    Period size: 60  Copynumber: 5.5  Consensus size: 60

        109 AGAGAAAGTT

                  *     *     *       *           *                     
        119 GGTGTCAGCCATTGCATGACCAACACTAAAAAATTTGATTTTTTTTATCAGATAAATAAG
          1 GGTGTCGGCCATGGCATGGCCAACACAAAAAAATTTGAATTTTTTTATCAGATAAATAAG

                    *                 **                              *    
        179 GGTGTCGGTCATGGCATGGCCAACACCCAAAAATTT-AATTTTTTTATTCAGATAAAAAAAGG
          1 GGTGTCGGCCATGGCATGGCCAACACAAAAAAATTTGAATTTTTTTA-TCAGAT-AAATAA-G

                   **           *                    *        **          
        241 GGTGTCGATCATGGCATGGCTAACACAAAAAAAATTTGAAAATTTTTTATTTGATAAAT-AG
          1 GGTGTCGGCCATGGCATGGCCAACAC-AAAAAAATTTG-AATTTTTTTATCAGATAAATAAG

                  *             *                              *  *   *    
        302 GGTTGTTGGCCATGGCATGGTCAACACCAAAAAAA-TTGAA-TTTTTTATCTGACAAAAAAGG
          1 GG-TGTCGGCCATGGCATGGCCAACA-CAAAAAAATTTGAATTTTTTTATCAGATAAATAA-G

                  *     *    * *                  *                   * 
        363 GGTGTCAGCCATTGCATAGACAACACAAAAAAATTTGATTTTTTTTATCA-ATAAATAGG
          1 GGTGTCGGCCATGGCATGGCCAACACAAAAAAATTTGAATTTTTTTATCAGATAAATAAG

                   *    *                    
        422 GGTGTCGACCATCGCATGGCCAACACAAAAAAA
          1 GGTGTCGGCCATGGCATGGCCAACACAAAAAAA

        455 ATTAAAATTT


Statistics
Matches: 225,  Mismatches: 39, Indels: 25
        0.78            0.13        0.09

Matches are distributed among these distances:
  59   60  0.27
  60   66  0.29
  61   23  0.10
  62   51  0.23
  63   12  0.05
  64    4  0.02
  65    9  0.04

ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29


Consensus pattern (60 bp):   
GGTGTCGGCCATGGCATGGCCAACACAAAAAAATTTGAATTTTTTTATCAGATAAATAAG

Found at i:1117 original size:24 final size:24

Alignment explanation


    Indices: 1090--1136  Score: 60
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       1080 GAGTTAATGT

                           *         
       1090 GTTAAA-AATATTAATTAAAAAAAA
          1 GTTAAACAATA-TAAATAAAAAAAA

                                   
       1114 GTTAAAGCAATATAAATAAAAAA
          1 GTTAAA-CAATATAAATAAAAAA

       1137 TAAAAAAGTG


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  24    6  0.30
  25   10  0.50
  26    4  0.20

ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26


Consensus pattern (24 bp):   
GTTAAACAATATAAATAAAAAAAA

Found at i:1415 original size:29 final size:29

Alignment explanation


    Indices: 1351--1415  Score: 69
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       1341 TTTAGCTAAA

                                        *
       1351 ATTAAAATCGACATAATCTGATAAATTTT
          1 ATTAAAATCGACATAATCTGATAAATTTG

             **        **                 
       1380 AAAAAAATCGATTTAATCTGAT-AATTATG
          1 ATTAAAATCGACATAATCTGATAAATT-TG

                   
       1409 ATTAAAA
          1 ATTAAAA

       1416 ATCAACATTT


Statistics
Matches: 28,  Mismatches: 7, Indels: 2
        0.76            0.19        0.05

Matches are distributed among these distances:
  28    4  0.14
  29   24  0.86

ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35


Consensus pattern (29 bp):   
ATTAAAATCGACATAATCTGATAAATTTG

Found at i:6397 original size:19 final size:19

Alignment explanation


    Indices: 6373--6409  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       6363 TTATTCCGCT

                               
       6373 CTACTTTAATTTAATTTTA
          1 CTACTTTAATTTAATTTTA

                   **         
       6392 CTACTTTTCTTTAATTTT
          1 CTACTTTAATTTAATTTT

       6410 TTCAATATTT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62


Consensus pattern (19 bp):   
CTACTTTAATTTAATTTTA

Found at i:9538 original size:12 final size:12

Alignment explanation


    Indices: 9521--9545  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       9511 TGCTCTTTTA

                        
       9521 AAAAAAAAAAAG
          1 AAAAAAAAAAAG

                        
       9533 AAAAAAAAAAAG
          1 AAAAAAAAAAAG

             
       9545 A
          1 A

       9546 CTAGTTTTAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00


Consensus pattern (12 bp):   
AAAAAAAAAAAG
Done.